All Stories

  1. Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond

    Article • Nature Communications, September 2025, Springer Science + Business Media

    Altuna A, Björn Grüning

  2. Ten Common Misconceptions About Galaxy (and Why They Are Wrong!

    Article • September 2025, MDPI AG

    Björn Grüning

  3. Open-Source and FAIR Research Software for Proteomics

    Article • Journal of Proteome Research, April 2025, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, Björn Grüning

  4. FAIR Digital Objects for Seamless Research Data Management for Researchers and Higher Education Institutions

    Article • Open Conference Proceedings, March 2025, TIB Open Publishing

    Björn Grüning

  5. PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking

    Article • GigaScience, January 2025, Oxford University Press (OUP)

    Björn Grüning

  6. Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

    Article • December 2024, Cold Spring Harbor Laboratory Press

    Björn Grüning

  7. PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking

    Article • June 2024, Cold Spring Harbor Laboratory Press

    Björn Grüning

  8. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

    Article • Nucleic Acids Research, May 2024, Oxford University Press (OUP)

    Krzysztof Poterlowicz, Matúš Kalaš, Björn Grüning

  9. Enhancing the image analysis community in Galaxy

    Article • April 2024, Center for Open Science

    Matúš Kalaš, Björn Grüning

  10. Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

    Article • Microbial Genomics, February 2024, Society for General Microbiology

    Björn Grüning

  11. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

    Article • Nature Biotechnology, January 2024, Springer Science + Business Media

    Björn Grüning

  12. blast2galaxy: a CLI and Python API for BLAST+ and DIAMOND searches on Galaxy servers

    Article • Bioinformatics Advances, January 2024, Oxford University Press (OUP)

    Björn Grüning

  13. Conda, Container and Bots

    Article • Proceedings of the Conference on Research Data Infrastructure, September 2023, TIB Open Publishing

    Björn Grüning

  14. EOSC-Life Workflow Collaboratory for the Life Sciences

    Article • Proceedings of the Conference on Research Data Infrastructure, September 2023, TIB Open Publishing

    Björn Grüning

  15. Galaxy and RDM

    Article • Proceedings of the Conference on Research Data Infrastructure, September 2023, TIB Open Publishing

    Björn Grüning

  16. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Björn Grüning

  17. Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

    Article • April 2023, Cold Spring Harbor Laboratory Press

    Björn Grüning

  18. Activator-blocker model of transcriptional regulation by pioneer-like factors

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Björn Grüning

  19. An accessible infrastructure for artificial intelligence using a Docker-based JupyterLab in Galaxy

    Article • GigaScience, December 2022, Oxford University Press (OUP)

    Björn Grüning

  20. Transformer-based tool recommendation system in Galaxy

    Article • December 2022, Cold Spring Harbor Laboratory Press

    Björn Grüning

  21. Community-driven ELIXIR activities in single-cell omics

    Article • F1000Research, July 2022, Faculty of 1000, Ltd.

    Björn Grüning

  22. Packaging research artefacts with RO-Crate

    Article • Data Science, July 2022, IOS Press

    Prof Carole A Goble, Björn Grüning, Dr Peter m Sefton

  23. MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone

    Article • Journal of Proteome Research, May 2022, American Chemical Society (ACS)

    Dr Oliver Schilling, Björn Grüning

  24. Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease

    Article • Journal of Cheminformatics, April 2022, Springer Science + Business Media

    Björn Grüning

  25. Ten simple rules for making a software tool workflow-ready

    Article • PLoS Computational Biology, March 2022, PLOS

    Björn Grüning

  26. Planemo: a command-line toolkit for developing, deploying, and executing scientific data analyses

    Article • March 2022, Cold Spring Harbor Laboratory Press

    Björn Grüning

  27. Pluripotency factors determine gene expression repertoire at zygotic genome activation

    Article • Nature Communications, February 2022, Springer Science + Business Media

    Björn Grüning

  28. MaxQuant and MSstats in Galaxy enable reproducible cloud-based analysis of quantitative proteomics experiments for everyone

    Article • January 2022, Cold Spring Harbor Laboratory Press

    Dr Oliver Schilling, Björn Grüning

  29. Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework

    Article • GigaScience, January 2022, Oxford University Press (OUP)

    Dr Oliver Schilling, Björn Grüning

  30. Loop detection using Hi-C data with HiCExplorer

    Article • GigaScience, January 2022, Oxford University Press (OUP)

    Björn Grüning

  31. Democratizing Data-Independent Acquisition Proteomics Analysis on Public Cloud Infrastructures Via The Galaxy Framework

    Article • July 2021, Cold Spring Harbor Laboratory Press

    Dr Oliver Schilling, Björn Grüning

  32. A SARS-CoV-2 sequence submission tool for the European Nucleotide Archive

    Article • Bioinformatics, June 2021, Oxford University Press (OUP)

    Björn Grüning

  33. Galaxy-ML: An accessible, reproducible, and scalable machine learning toolkit for biomedicine

    Article • PLoS Computational Biology, June 2021, PLOS

    Björn Grüning

  34. Robust and efficient single-cell Hi-C clustering with approximate k-nearest neighbor graphs

    Article • Bioinformatics, May 2021, Oxford University Press (OUP)

    Björn Grüning

  35. A constructivist-based proposal for bioinformatics teaching practices during lockdown

    Article • PLoS Computational Biology, May 2021, PLOS

    Björn Grüning

  36. Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Björn Grüning

  37. BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers

    Article • Journal of Proteome Research, February 2021, American Chemical Society (ACS)

    Dr. Yasset Perez-Riverol, Björn Grüning, DR Juan Antonio Vizcaino

  38. A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)

    Article • February 2021, Cold Spring Harbor Laboratory Press

    Björn Grüning

  39. ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data

    Article • GigaScience, January 2021, Oxford University Press (OUP)

    Björn Grüning

  40. Metaproteomics Analysis of SARS-CoV-2-Infected Patient Samples Reveals Presence of Potential Coinfecting Microorganisms

    Article • Journal of Proteome Research, January 2021, American Chemical Society (ACS)

    Björn Grüning

  41. Tool recommender system in Galaxy using deep learning

    Article • GigaScience, January 2021, Oxford University Press (OUP)

    Björn Grüning

  42. Adding software to package management systems can increase their citation by 280%

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Björn Grüning

  43. Survey of metaproteomics software tools for functional microbiome analysis

    Article • PLOS One, November 2020, PLOS

    Dr Pratik Dilip Jagtap, Björn Grüning

  44. NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy

    Article • GigaScience, October 2020, Oxford University Press (OUP)

    J HAYS, Björn Grüning

  45. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

    Article • F1000Research, September 2020, Faculty of 1000, Ltd.

    Björn Grüning

  46. Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

    Article • Journal of Cheminformatics, September 2020, Springer Science + Business Media

    Björn Grüning

  47. Training Infrastructure as a Service

    Article • August 2020, Cold Spring Harbor Laboratory Press

    Björn Grüning

  48. No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics

    Article • PLoS Pathogens, August 2020, PLOS

    Björn Grüning

  49. BioContainers Registry: searching for bioinformatics tools, packages and containers

    Article • July 2020, Cold Spring Harbor Laboratory Press

    Dr. Yasset Perez-Riverol, Björn Grüning, DR Juan Antonio Vizcaino

  50. Accessible, Reproducible, and Scalable Machine Learning for Biomedicine

    Article • June 2020, Cold Spring Harbor Laboratory Press

    Björn Grüning

  51. The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform

    Article • Journal of Cheminformatics, June 2020, Springer Science + Business Media

    Björn Grüning

  52. Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

    Article • May 2020, Cold Spring Harbor Laboratory Press

    Björn Grüning

  53. Ewastools: Infinium Human Methylation BeadChip pipeline for population epigenetics integrated into Galaxy

    Article • GigaScience, May 2020, Oxford University Press (OUP)

    Krzysztof Poterlowicz, Dr Gillian Westgate, Björn Grüning

  54. Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization

    Article • Nucleic Acids Research, April 2020, Oxford University Press (OUP)

    Björn Grüning

  55. Pluripotency factors determine gene expression repertoire at zygotic genome activation

    Article • February 2020, Cold Spring Harbor Laboratory Press

    Björn Grüning

  56. Survey of metaproteomics software tools for functional microbiome analysis

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Björn Grüning

  57. GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering

    Article • GigaScience, December 2019, Oxford University Press (OUP)

    Björn Grüning

  58. Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

    Article • GigaScience, December 2019, Oxford University Press (OUP)

    Dr Oliver Schilling, Björn Grüning

  59. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR

    Article • F1000Research, November 2019, Faculty of 1000, Ltd.

    Björn Grüning

  60. The RNA workbench 2.0: next generation RNA data analysis

    Article • Nucleic Acids Research, May 2019, Oxford University Press (OUP)

    Björn Grüning

  61. Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

    Article • May 2019, Cold Spring Harbor Laboratory Press

    Dr Oliver Schilling, Björn Grüning

  62. Software engineering for scientific big data analysis

    Article • GigaScience, May 2019, Oxford University Press (OUP)

    Björn Grüning

  63. Recommendations for the packaging and containerizing of bioinformatics software

    Article • F1000Research, March 2019, Faculty of 1000, Ltd.

    Björn Grüning, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

  64. Empowering the annotation and discovery of structured RNAs with scalable and accessible integrative clustering

    Article • February 2019, Cold Spring Harbor Laboratory Press

    Björn Grüning

  65. Pou5f3, SoxB1, and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation

    Article • Genome Research, January 2019, Cold Spring Harbor Laboratory Press

    Björn Grüning

  66. Impact of angiogenic activation and inhibition on miRNA profiles of human retinal endothelial cells

    Article • Experimental Eye Research, January 2019, Elsevier

    Björn Grüning

  67. Update on the moFF Algorithm for Label-Free Quantitative Proteomics

    Article • Journal of Proteome Research, December 2018, American Chemical Society (ACS)

    Björn Grüning

  68. Recommendations for the packaging and containerizing of bioinformatics software

    Article • F1000Research, June 2018, Faculty of 1000, Ltd.

    Mr Rafael C Jimenez, Björn Grüning, Susheel Varma, Pablo Moreno, Dr. Yasset Perez-Riverol

  69. Pou5f3, SoxB1 and Nanog remodel chromatin on High Nucleosome Affinity Regions at Zygotic Genome Activation

    Article • June 2018, Cold Spring Harbor Laboratory Press

    Björn Grüning

  70. Parkour LIMS: facilitating high-quality sample preparation in next generation sequencing

    Article • June 2018, Cold Spring Harbor Laboratory Press

    Björn Grüning

  71. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

    Article • Nucleic Acids Research, May 2018, Oxford University Press (OUP)

    Björn Grüning

  72. High-resolution TADs reveal DNA sequences underlying genome organization in flies

    Article • Nature Communications, January 2018, Nature

    Björn Grüning

  73. ENASearch: A Python library for interacting with ENA's API

    Article • The Journal of Open Source Software, October 2017, The Open Journal

    Björn Grüning

  74. Practical computational reproducibility in the life sciences

    Article • October 2017, Cold Spring Harbor Laboratory Press

    Björn Grüning

  75. EBF1 binds to EBNA2 and promotes the assembly of EBNA2 chromatin complexes in B cells

    Article • PLoS Pathogens, October 2017, PLOS

    Björn Grüning

  76. Recent advances in RNA folding

    Article • Journal of Biotechnology, July 2017, Elsevier

    Björn Grüning

  77. Four simple recommendations to encourage best practices in research software

    Article • F1000Research, June 2017, Faculty of 1000, Ltd.

    Dr Monther Alhamdoosh, Mr Rafael C Jimenez, Mr Neil P Chue Hong, Professor Josep Ll. Gelpi, Prof Carole A Goble, Rob Hooft, Daniel S Katz, Mr Federico López Gómez, Dr Sonika Tyagi, Sonika Tyagi, Mateusz Kuzak, Allegra Via, Xiaochuan (Harry) Wang, Montserrat Gonzalez, Björn Grüning, Andrew Treloar, Nathan Watson-Haigh, Dr. Yasset Perez-Riverol

  78. The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

    Article • Nucleic Acids Research, June 2017, Oxford University Press (OUP)

    Björn Grüning, Altuna A

  79. Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers

    Article • PLoS Computational Biology, May 2017, PLOS

    Björn Grüning

  80. RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation

    Article • Journal of Biotechnology, May 2017, Elsevier

    Björn Grüning

  81. ReGaTE: Registration of Galaxy Tools in Elixir

    Article • GigaScience, April 2017, Oxford University Press (OUP)

    Björn Grüning, Matúš Kalaš

  82. BioContainers: an open-source and community-driven framework for software standardization

    Article • Bioinformatics, March 2017, Oxford University Press (OUP)

    Björn Grüning, Mr Rafael C Jimenez, Dr. Yasset Perez-Riverol

  83. GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders

    Article • Genetics Research, January 2017, Cambridge University Press

    Tobias Hornig, Björn Grüning

  84. 5'-Hydroxymethylcytosine Precedes Loss of CpG Methylation in Enhancers and Genes Undergoing Activation in Cardiomyocyte Maturation

    Article • PLOS One, November 2016, PLOS

    Björn Grüning

  85. PubMedPortable: A Framework for Supporting the Development of Text Mining Applications

    Article • PLOS One, October 2016, PLOS

    Björn Grüning

  86. Enhancing pre-defined workflows withad hocanalytics using Galaxy, Docker and Jupyter

    Article • September 2016, Cold Spring Harbor Laboratory Press

    Björn Grüning

  87. Echinocandin B biosynthesis: a biosynthetic cluster from Aspergillus nidulans NRRL 8112 and reassembly of the subclusters Ecd and Hty from Aspergillus pachycristatus NRRL 11440 reveals a single coherent gene cluster

    Article • BMC Genomics, August 2016, Springer Science + Business Media

    Björn Grüning

  88. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

    Article • Nucleic Acids Research, May 2016, Oxford University Press (OUP)

    Björn Grüning

  89. deepTools2: a next generation web server for deep-sequencing data analysis

    Article • Nucleic Acids Research, April 2016, Oxford University Press (OUP)

    Björn Grüning

  90. MicroRNA Profiling in Aqueous Humor of Individual Human Eyes by Next-Generation Sequencing

    Article • Investigative Ophthalmology & Visual Science, April 2016, Association for Research in Vision and Ophthalmology (ARVO)

    Björn Grüning

  91. An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology

    Article • Cancer Informatics, April 2016, Libertas Academica, Ltd.

    Björn Grüning

  92. Tools and data services registry: a community effort to document bioinformatics resources

    Article • Nucleic Acids Research, November 2015, Oxford University Press (OUP)

    Mr Rafael C Jimenez, Björn Grüning, Dr Tunca Dogan, Matúš Kalaš

  93. DOT1L Activity Promotes Proliferation and Protects Cortical Neural Stem Cells from Activation of ATF4-DDIT3-Mediated ER Stress In Vitro

    Article • Stem Cells, September 2015, Wiley

    Björn Grüning

  94. NCBI BLAST+ integrated into Galaxy

    Article • GigaScience, August 2015, Oxford University Press (OUP)

    Björn Grüning

  95. Anatomy of BioJS, an open source community for the life sciences

    Article • eLife, July 2015, eLife

    Mr Bruno Vieira, Björn Grüning, Saket Choudhary

  96. Deciphering the Epigenetic Code of Cardiac Myocyte TranscriptionNovelty and Significance

    Article • Circulation Research, June 2015, Wolters Kluwer Health

    Björn Grüning

  97. The Purchasable Chemical Space: A Detailed Picture

    Article • Journal of Chemical Information and Modeling, May 2015, American Chemical Society (ACS)

    Björn Grüning

  98. NCBI BLAST+ integrated into Galaxy

    Article • January 2015, Cold Spring Harbor Laboratory Press

    Björn Grüning

  99. Dynamic DNA methylation orchestrates cardiomyocyte development, maturation and disease

    Article • Nature Communications, October 2014, Nature

    Björn Grüning

  100. Autosomal dominant immune dysregulation syndrome in humans with CTLA4 mutations

    Article • Nature Reports Stem Cells, October 2014, Nature

    Björn Grüning

  101. PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering

    Article • Bioinformatics, July 2014, Oxford University Press (OUP)

    Björn Grüning

  102. deepTools: a flexible platform for exploring deep-sequencing data

    Article • Nucleic Acids Research, May 2014, Oxford University Press (OUP)

    Björn Grüning

  103. Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling inStreptomyces

    Article • Journal of the American Chemical Society, April 2014, American Chemical Society (ACS)

    Björn Grüning

  104. Dynamic information system for small molecules

    Article • Journal of Cheminformatics, January 2014, Springer Science + Business Media

    Björn Grüning

  105. ChemicalToolBoX and its application on the study of the drug like and purchasable space

    Article • Journal of Cheminformatics, January 2014, Springer Science + Business Media

    Björn Grüning

  106. Characterization and Phylogenetic Analysis of the Mitochondrial Genome of Glarea lozoyensis Indicates High Diversity within the Order Helotiales

    Article • PLOS One, September 2013, PLOS

    Björn Grüning

  107. Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

    Article • PeerJ, September 2013, PeerJ

    Björn Grüning

  108. Draft Genome Sequence of Streptomyces viridochromogenes Strain Tu57, Producer of Avilamycin

    Article • Genome Announcements, June 2013, ASM Journals

    Björn Grüning

  109. StreptomeDB: a resource for natural compounds isolated from Streptomyces species

    Article • Nucleic Acids Research, November 2012, Oxford University Press (OUP)

    Björn Grüning

  110. Genome Sequence of the Fungus Glarea lozoyensis: the First Genome Sequence of a Species from the Helotiaceae Family

    Article • Eukaryotic Cell, February 2012, ASM Journals

    Björn Grüning

  111. Mining and evaluation of molecular relationships in literature

    Article • Bioinformatics, January 2012, Oxford University Press (OUP)

    Björn Grüning

  112. Small-molecule conversion of toxic oligomers to nontoxic β-sheet–rich amyloid fibrils

    Article • Nature Chemical Biology, November 2011, Nature

    Björn Grüning

  113. Genome Sequence of Streptomyces sp. Strain Tu6071

    Article • Journal of Bacteriology, June 2011, ASM Journals

    Björn Grüning

  114. Compounds In Literature (CIL): screening for compounds and relatives in PubMed

    Article • Bioinformatics, March 2011, Oxford University Press (OUP)

    Björn Grüning

  115. RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils

    Article • Nucleic Acids Research, May 2009, Oxford University Press (OUP)

    Björn Grüning

  116. SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

    Article • Nucleic Acids Research, May 2009, Oxford University Press (OUP)

    Björn Grüning

  117. SuperScent--a database of flavors and scents

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Björn Grüning

  118. SuperToxic: a comprehensive database of toxic compounds

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Björn Grüning

  119. Voronoia: analyzing packing in protein structures

    Article • Nucleic Acids Research, January 2009, Oxford University Press (OUP)

    Björn Grüning